Genetic Dissection of Seed Storability and Validation of Candidate Gene Associated with Antioxidant Capability in Rice (Oryza sativa L.)

Abstract

Seed storability, defined as the ability to remain alive during storage, is an important agronomic and physiological characteristic, but the underlying genetic mechanism remains largely unclear. Here, we report quantitative trait loci (QTLs) analyses for seed storability using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that was derived from a cross of a japonica cultivar, Nipponbare, and an indica cultivar, 9311. Seven putative QTLs were identified for seed storability under natural storage, each explaining 3.6–9.0% of the phenotypic variation in this population. Among these QTLs, qSS1 with the 9311 alleles promoting seed storability was further validated in near-isogenic line and its derived-F2 population. The other locus (qSS3.1) for seed storability colocalized with a locus for germination ability under hydrogen peroxide, which is recognized as an oxidant molecule that causes lipid damage. Transgenic experiments validated that a candidate gene (OsFAH2) resides the qSS3.1 region controlling seed storability and antioxidant capability. Overexpression of OsFAH2 that encodes a fatty acid hydroxylase reduced lipid preoxidation and increased seed storability. These findings provide new insights into the genetic and physiological bases of seed storability and will be useful for the improvement of seed storability in rice.

Genetic Dissection and Validation of Chromosomal Regions for Transmission Ratio Distortion in Intersubspecific Crosses of Rice

“…The BIL population and chromosome segment substitution line (CSSL-derived) population were used to dissect the genetic basis of TRD in rice. The BILs, which included 437 lines, were developed by single-seed descent from the cross between two genome-sequenced rice cultivars, the japonica variety Nipponbare (NIP) and the elite indica restorer line 9311 (Yuan et al, 2019). Briefly, NIP (male) was crossed with 9311 (female), and the F 1 was then backcrossed to 9311 (female) to obtain BC 1 F 1 lines.…”

“…Genomic DNA was extracted from young seedling leaves using the CTAB method as described previously (Murray and Thompson, 1980). The 437 BILs were genotyped using a genotyping-by-sequencing (GBS) strategy (Yuan et al, 2019). The GBS library were generated as described in a previous report (Elshire et al, 2011), where the genomic DNA from each of the BILs was digested with MseI, followed by end blunting, dATP addition at the 3 end, and ligation of Y-adapters.…”

Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

“…S1). The genomic DNA from each line of BILs was extracted and subjected to genotyping as described previously (Yuan et al 2019 ). To validate the effect of qSD3.2 , one CSSL (NY38) that carried a 1.6-Mb introduced NIP segment surrounding qSD3.2 on chromosome 3 and a background NIP segment on chromosome 10 was crossed with 9311 to generate an F 2 population (hereafter referred to as the NY38-derived population).…”

“…All dishes were placed in a growth chamber (Dongnan, Ningbo, China) at 25 °C under a 16 h light/ 8 h dark cycle. The number of germinated seeds was monitored and counted every 24 h for seven consecutive days to construct cumulative germination curves (Yuan et al 2019 ). Freshly harvested seeds were treated at 43 °C for 3 days to break seed dormancy as described previously (Li et al 2011 ).…”

“…For the 437 BILs, a genotyping-by-sequencing (GBS) strategy with high-throughput genotyping was adopted to confirm the genotypes (Yuan et al 2019 ). A total of 49,890 high-quality single-nucleotide polymorphisms (SNPs) were identified after filtering out the low-quality SNPs, followed by Bayesian inference (Yu et al 2011 ).…”